compareComplex             package:ScISI             R Documentation

_A _f_u_n_c_t_i_o_n _t_o _c_o_m_p_a_r_e _t_w_o _b_i_p_a_r_t_i_t_e _g_r_a_p_h _m_a_t_r_i_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     The 'compareComplex' function takes two bipartite graph matrix
     representations and calculates three statistics between all pairs
     of complexes, C-i and K-j: (1) the intersection between C-i and
     K-j, (2) the proteins in C-i and not in K-j, (3) the proteins in
     K-j and not in C-i. These stats are later used to calculate
     Jaccard and Dice-Sorenson Coefficients as well as probability
     distributions of a protein p in a complex C.

_U_s_a_g_e:

     compareComplex(BGMat1, BGMat2)

_A_r_g_u_m_e_n_t_s:

  BGMat1: The first bipartite graph matrix

  BGMat2: The second bipartite graph matrix

_D_e_t_a_i_l_s:

     The main point to remember is that we don't compare complexes
     within the same matrix. We only compare pairs of complexes from
     the BGMat1 and BGMat2. The 'runCompareComplex' function must be
     called first since all the labelled vertices present in BGMat1
     must be present in the BGMat2 and vice versa so a true comparison
     can be made.

_V_a_l_u_e:

     A list with the following entries:

intersect: A matrix of pairwise intersections of the complexes of
          BGMat1 and BGMat2

 cminusk: A matrix of the setdiff of the complexes of BGMat1 and those
          of BGMat2

 kminusc: A matric of the setdiff of the complexes of BGMat2 and those
          of BGMat1

_A_u_t_h_o_r(_s):

     Tony Chiang

